Computational protocol: Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process

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Protocol publication

[…] A phylogeny for all species found in the 90 plots was obtained by using the informatics tool Phylomatic (available at http://www.phylodiversity.net). Phylomatic uses the Angiosperm Phylogeny Group’s APGIII consensus tree (R20120829) as a backbone onto which species are added based on their taxonomy. Branch lengths for each tree species were estimated using the BLADJ algorithm, and node dates were estimated from Wikstrom et al.. We used Faith’s phylogenetic diversity (PD) metric to quantify the phylogenetic alpha diversity of each plot. Faith’s PD has the advantage of being phylogenetic diversity metric in conservation research.We used the net relatedness index (NRI) and Nearest Taxon Index (NTI) to quantify the degree of phylogenetic relatedness among species within each plot. These metrics were estimated with the COMSTRUCT algorithm implemented in Phylocom. NRI measures the standardized effect size of the mean phylogenetic distance (MPD), which estimates the average phylogenetic relatedness between all possible pairs of taxa in a community. The NTI calculates the mean nearest phylogenetic neighbor among the individuals in a community. Random communities were generated by drawing species from phylogeny pool, while maintaining per-plot species richness and the frequency of species occurrence among plots. The species pool used in these randomizations included all the species occurring in the study region. NRI and NTI are defined as follows: where MNTD/MPDobserved is the observed MNTD/MPD, MNTD/MPDrandomized is the expected MNTD/MPD of the randomized assemblages (n = 999) and sdMNTD/MPDrandomized is the standard deviation of the MNTD/MPD for the randomized assemblages. A positive NTI/NRI value indicates that MNTD/MPD is lower than that expected by chance and that phylogenetic clustering of species occurs. Conversely, a negative NTI/NRI value indicates phylogenetic overdispersion. […]

Pipeline specifications

Software tools Phylomatic, Phylocom
Application Phylogenetics